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- PDB-3v9t: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -

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Basic information

Entry
Database: PDB / ID: 3v9t
TitleCrystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator
Components
  • Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION/TRANSCRIPTION REGULATOR / three-layered alpha-helical sandwich / transcription regulation / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / temperature homeostasis / WW domain binding / response to starvation / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / lncRNA binding / response to muscle activity / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / intracellular glucose homeostasis / negative regulation of SMAD protein signal transduction / fatty acid oxidation / response to dietary excess / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / adipose tissue development / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / BMP signaling pathway / long-chain fatty acid transport / brown fat cell differentiation / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / energy homeostasis / cell maturation / digestion / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / positive regulation of gluconeogenesis / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / SUMOylation of transcription cofactors / RNA splicing / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / nuclear receptor binding / Regulation of PTEN gene transcription / positive regulation of apoptotic signaling pathway / gluconeogenesis / transcription coregulator binding / respiratory electron transport chain / transcription coregulator activity / mitochondrion organization / transcription initiation at RNA polymerase II promoter / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway / fatty acid metabolic process / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-17L / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMatsui, Y. / Hanzawa, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Substituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPAR(gamma) partial agonists
Authors: Furukawa, A. / Arita, T. / Fukuzaki, T. / Satoh, S. / Mori, M. / Honda, T. / Matsui, Y. / Wakabayashi, K. / Hayashi, S. / Araki, K. / Ohsumi, J.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
C: Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0093
Polymers34,4802
Non-polymers5301
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.889, 54.614, 66.797
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32412.576 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 234-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 2067.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-17L / (9aS)-8-acetyl-N-[(3-ethoxynaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide


Mass: 529.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium thiocyanate, Tris-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 37110 / Num. obs: 36869 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 %
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Num. unique all: 3491 / % possible all: 94.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LMP

3lmp


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.838 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21878 3392 10.1 %RANDOM
Rwork0.20176 ---
obs0.2035 30353 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.561 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å2-0.3 Å2
2---0.68 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 39 219 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222209
X-RAY DIFFRACTIONr_bond_other_d0.0010.021493
X-RAY DIFFRACTIONr_angle_refined_deg1.0032.0212980
X-RAY DIFFRACTIONr_angle_other_deg0.80433685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.375264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58725.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26315427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.128158
X-RAY DIFFRACTIONr_chiral_restr0.0560.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5411.51335
X-RAY DIFFRACTIONr_mcbond_other0.0941.5535
X-RAY DIFFRACTIONr_mcangle_it1.06922157
X-RAY DIFFRACTIONr_scbond_it1.6133874
X-RAY DIFFRACTIONr_scangle_it2.7414.5823
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 257 -
Rwork0.251 2218 -
obs--99.92 %

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